I will be in Alaska in a few weeks for a photography trip focused on whales, seals, eagles & glaciers in Glacier Bay. Can anyone provide general advice on photographing whales and settings for shooting from a boat (90').
I haven't shot whales in Alaska but I have in British Columbia, Mexico and Hawaii from similar sized boats.
There isn't really anything special unless you are trying to shoot a breach - see below.
You don't need a particularly long lens since whales are big. Your 100-400mm should be fine.
You can use single shot focusing since the whales don't move much horizontally. I would probably use a central group of focus points just in case you see a breach. Maybe shoot at 3-5 fps if you are going to shoot tail fluking, lunge feeding or bubble feeding. Even breaches don't really require more than 5 fps. Whales move a lot slower than, say, a peregrine falcon. :-D
You don't need a really high shutter speed for most whale shots and 1/500 is fine unless you are shooting breaches when I would try to go to 1/1000+. If you are shooting groups of whales bubble feeding then you might want a decent depth of field so you may need to stop down.
I have tried using a CPL and found that it didn't do anything except take away light. On the other hand I have found it very useful to use polarizing sunglasses in certain situations, especially when dolphins are around the boat. It just enables you to see a little further under the water and gives you a fraction of a second more to spot a jump.
If you get a chance to shoot breaches then, unless you are lucky enough to find a whale doing a series of breaches, the biggest problem that you will have will be just getting the whale in the VF because the breach will come out of nowhere. So try to keep the camera up to your eyes as much as you can and try to get a position in the boat where you can scan through a wide angle. Adult breaches last 2-3 seconds so you don't need a high fps rate, just very fast reactions to get the camera on the whale and lots and lots of luck. Use single shot focusing and don't zoom in too far - you don't want to get the camera on a breach 100 yds from the boat and then find that you have cut off part of the whale's head. Shoot a bit wider and crop later if the whale is further away.
Resist the temptation to take hundreds of shots of whales surfacing to breathe or even tail flukes when they dive. You will find when you get back that you only need one or two tail fluke shots and probably only one of a whale's back for your album. Unless you are shooting in in very interesting light the shots that you are looking for are lunge feeding, bubble feeding and breaches.
I personally have rarely had problems with spray when shooting from a 90' boat but it would be worth taking some kind of rain sleeve (and possibly having a protective filter on the front of the lens) in case you get good shooting opportunities in rough seas.
That is all that I can think of for the moment. Hopefully somebody who has shot in Alaska will be able to give you more specific advice.